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Microsatellite Marker for Genetic Variation Analysis in Local Chili Pepper (Capsicum frutescens L.) Induced by Ethyl Methane Sulfonate (EMS) Ria Reinnata Juliandari; Retno Mastuti; Estri Laras Arumningtyas
Journal of Tropical Life Science Vol. 9 No. 2 (2019)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.09.02.08

Mutation using Ethyl Methane Sulfonate (EMS) is a simple and quick method to produce genetic variation in chili pepper. In this study, a total of 3 genotypes of local chili pepper (Capsicum frutescens L.), i.e. Genotype 2 (G2), Genotype 7 (G7), and Genotype 11 (G11) were induced by EMS with concentrations of 0% (K0), 0.01% (K1), 0.02% (K2), and 0.04% (K3). Genetic variation analysis in mutant was performed based on 3 microsatellite markers CA 19, CA 27, CA 62. Those molecular markers successfully detected the genetic variation in chili pepper mutant based on the number and size of microsatellite alleles variation. The 3 genotypes of chili pepper mutant produced a total of 15 alleles with the average Polymorphism Information Content (PIC) value of 0.82. Compared to the control plant, genetic variations in genome level were observed in local chili pepper. Furthermore, the treatment of EMS with concentration of 0.04% produced the most notable genetic variation in 3 genotypes of local chili pepper.Â

Variation of Fruit Color in Cakra Hijau, G1/M8 and HV-149 Chilli Pepper Cultivar: Physiology and Molecular Approach: Variation of Fruit Color in Cakra Hijau, G1/M8 and HV-149 Cultivar Arumingtyas, Estri Laras; Zakiyah, 'Ainun Sayyidah; Monica, Rosina; Siswanto, Dian
Journal of Tropical Life Science Vol. 13 No. 3 (2023)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.13.03.13

The fruit color of chili pepper is an important characteristic in identification and classification and is often used as the basis for determining consumer preferences. Information on the relationship between chili fruit color and its molecular profile is very important in supporting selection activities in plant breeding. This study aims to identify genetic diversity associated with the fruit color of three genotypes of chili (Capsicum frutescens L.): Cakra Hijau, HV-149 and G1/M8, using Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeat (SSR). Morphological confirmation was carried out according to Capsicum descriptors. Nineteen RAPD markers and six SSR markers were used for genetic variability assessment. Genetic variation was analyzed using the unweighted pair group method with the arithmetic mean and the Jaccard similarity index. The three chili genotypes had different fruit colors at each maturation stage. The immature Cakra Hijau fruit is dark green and turns dark red as it ripens. The immature fruits of the G1/M8 line are light green and turn red when ripe. Finally, immature HV-149 fruits are dark green and yellow when ripe. The SSR markers used in this study were unable to show polymorphism. On the other hand, the RAPD marker successfully detected genetic variation in the three chili genotypes and resulted in a total of 49 alleles. The average value of polymorphic information content of the RAPD primers used ranged from 0 to 0.296, with the highest index indicated by OPA-1. The dendrogram shows the separation of the three genotypes into two main clusters, with the first cluster consisting of the HV-149 variety and the second cluster consisting of Cakra Hijau and G1/M8 lines. This study revealed that there are genetic variations based on the morphological characteristics of fruit color at each ripening stage and RAPD band profile. The RAPD marker was more effective than the SSR marker for identifying the genetic diversity of fruit color in the three chilies studied.

Genetic Diversity of Porang (Amorphophallus muelleri Blume) in Malang, East Java based on Morphology and Molecular Markers (ITS2, trnL, and matK): Genetic Diversity of Amorphophallus muelleri Blume in Malang Nensy Marantika, Riza; Arumingtyas, Estri Laras; Azrianingsih , Rodiyati
Journal of Tropical Life Science Vol. 15 No. 1 (2025)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.15.01.07

Porang (Amorphophallus muelleri) is an herbaceous plant belonging to the Araceae family that is distributed in Java, including the Malang region. This study aimed to determine the morphological and genetic variation of porang in the Malang region based on ITS2, trnL, and matK molecular markers. Porang samples were collected from seven populations in Malang district, i.e., Kasembon, Ngantang, Pujon, Dampit, Kalipare, Pagak, and Bantur. Observa-tions of porang included 27 morphological traits, and young leaves were ob-tained for DNA extraction. Then, ITS2, trnL, and matK were amplified using a specific primer pair. Morphological traits exhibited similarity in color, surface, shape, and petiole pattern, while differences were apparent in morphological size parameters. Porang petiole of all the populations in Malang is green with a white prismatic pattern and linear lines. The 438 bp ITS2 sequences con-tained 390 bp invariable sites and 48 bp variable sites, whereas the 555 bp trnL intron sequences consisted of 511 bp invariable sites and 44 bp variable sites, and the 738 bp matK sequences comprised 713 bp invariable sites and 25 bp variable sites. The ITS2 sequences of the seven porang populations had the highest number of variable sites compared with the trnL and matK sequences. The total number of haplotypes based on ITS2, trnL, and matK was 11, with a haplotype diversity value of 1.00. Haplotype 1–7 were A. muelleri, haplotype 8 was A. paeoniifolius, and haplotypes 9, 10, and 11 were A. bulbifer, A. konjac, and A. sumawongii, respectively (from Genbank). Fur-thermore, phylogenetic analysis using Maximum Likelihood, Neighbor Joining, and Maximum Parsimony based on the ITS2, trnL, and matK sequences showed consistent clades. Clade 1 comprises A. muelleri, which is divided into 3 subclades. Subclade 1 comprises Kasembon, Ngantang, Pagak, Dampit, subclade 2 comprises Kalipare and Pujon, and subclade 3 is Bantur. Clade 2 is A. bulbifer, and clade 3 consists of outgroups.

Variation of Fruit Color in Cakra Hijau, G1/M8 and HV-149 Chilli Pepper Cultivar: Physiology and Molecular Approach: Variation of Fruit Color in Cakra Hijau, G1/M8 and HV-149 Cultivar Arumingtyas, Estri Laras; Zakiyah, 'Ainun Sayyidah; Monica, Rosina; Siswanto, Dian
Journal of Tropical Life Science Vol. 13 No. 3 (2023)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.13.03.13

The fruit color of chili pepper is an important characteristic in identification and classification and is often used as the basis for determining consumer preferences. Information on the relationship between chili fruit color and its molecular profile is very important in supporting selection activities in plant breeding. This study aims to identify genetic diversity associated with the fruit color of three genotypes of chili (Capsicum frutescens L.): Cakra Hijau, HV-149 and G1/M8, using Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeat (SSR). Morphological confirmation was carried out according to Capsicum descriptors. Nineteen RAPD markers and six SSR markers were used for genetic variability assessment. Genetic variation was analyzed using the unweighted pair group method with the arithmetic mean and the Jaccard similarity index. The three chili genotypes had different fruit colors at each maturation stage. The immature Cakra Hijau fruit is dark green and turns dark red as it ripens. The immature fruits of the G1/M8 line are light green and turn red when ripe. Finally, immature HV-149 fruits are dark green and yellow when ripe. The SSR markers used in this study were unable to show polymorphism. On the other hand, the RAPD marker successfully detected genetic variation in the three chili genotypes and resulted in a total of 49 alleles. The average value of polymorphic information content of the RAPD primers used ranged from 0 to 0.296, with the highest index indicated by OPA-1. The dendrogram shows the separation of the three genotypes into two main clusters, with the first cluster consisting of the HV-149 variety and the second cluster consisting of Cakra Hijau and G1/M8 lines. This study revealed that there are genetic variations based on the morphological characteristics of fruit color at each ripening stage and RAPD band profile. The RAPD marker was more effective than the SSR marker for identifying the genetic diversity of fruit color in the three chilies studied.

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